TitleOrfM: A fast open reading frame predictor for metagenomic data.
Publication TypeJournal Article
Year of Publication2016
AuthorsWoodcroft B.J., Boyd JA, Tyson GW
JournalBioinformatics (Oxford, England)
Date Published2016 May 3
ISSN1367-4811
AbstractFinding and translating stretches of DNA lacking stop codons is a task common in the analysis of sequence data. However the computational tools for finding open reading frames are sufficiently slow that they are becoming a bottleneck as the volume of sequence data grows. This computational bottleneck is especially problematic in metagenomics when searching unassembled reads, or screening assembled contigs for genes of interest. Here we present OrfM, a tool to rapidly identify open reading frames (ORFs) in sequence data by applying the Aho-Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical ORFs to similar tools (’GetOrf’ and ’Translate’) but is five times faster. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers.

Address

Australian Centre for Ecogenomics
Level 5, Molecular Biosciences Bldg
University of Queensland
ST LUCIA QLD 4072
Brisbane, Australia

Stay connected

Copyright

© 2010-2017 Australian Centre for Ecogenomics